naturepoker
@binomicalabs.org
Binomica Labs independent researcher by day, warehouse worker by night
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@[email protected]
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@[email protected]
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Pinned
naturepoker
@binomicalabs.org
· Oct 21
Now that we have pinned posts:
I'm a self-taught biologist in #NYC studying the microbial tree of life with lots of long-read sequencing focus.
Most of my study is self-funded from warehouse and other odd jobs - I'm hoping to document paths to a working class, independent researcher for others.
I'm a self-taught biologist in #NYC studying the microbial tree of life with lots of long-read sequencing focus.
Most of my study is self-funded from warehouse and other odd jobs - I'm hoping to document paths to a working class, independent researcher for others.
Reposted by naturepoker
I also also have a standalone article, here: https://sciencedirect.com/science/article/abs/pii/S0160932718300528
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
November 24, 2025 at 4:58 PM
I also also have a standalone article, here: https://sciencedirect.com/science/article/abs/pii/S0160932718300528
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
Full disclosure: analysis to a certain extent changed by the time of the dissertation.
🌱🐋🧪 #histSTM #evobio 🐡
Drafting conference abstracts while fighting muscle aches from a warehouse shift. I think it's wonderful - it's good to think of a future where your welders and delivery drivers will still think of history and evolution of our universe, and independently make small thoughtful contributions.
November 24, 2025 at 10:36 PM
Drafting conference abstracts while fighting muscle aches from a warehouse shift. I think it's wonderful - it's good to think of a future where your welders and delivery drivers will still think of history and evolution of our universe, and independently make small thoughtful contributions.
Reposted by naturepoker
We are hiring! If you're interested in exploring the #biogeography of #prokaryotes using #genomics and #metagenomics, are interested in biology and geographic information systems, and are passionate about #OpenScience, this is for you! New PhD and PostDoc positions in my lab at Aalborg University
November 24, 2025 at 8:49 PM
We are hiring! If you're interested in exploring the #biogeography of #prokaryotes using #genomics and #metagenomics, are interested in biology and geographic information systems, and are passionate about #OpenScience, this is for you! New PhD and PostDoc positions in my lab at Aalborg University
Reposted by naturepoker
High-throughput DNA extraction from soil: experiences? best kits? best tools? If you had a decent chunk of money to throw at it, what system would you set up to make it fast and high quality? 🌾 🧪 🔬 🦠
November 24, 2025 at 1:15 PM
High-throughput DNA extraction from soil: experiences? best kits? best tools? If you had a decent chunk of money to throw at it, what system would you set up to make it fast and high quality? 🌾 🧪 🔬 🦠
Reposted by naturepoker
#OnThisDay in 1859, Charles Darwin's On the Origin of Species was first published.
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
November 24, 2025 at 11:26 AM
#OnThisDay in 1859, Charles Darwin's On the Origin of Species was first published.
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
Much of the original manuscript was used as scrap paper by Darwin's children. On the back of this painting of a house is an original manuscript page from Origin!
#CambridgeUniversityLibrary (DAR 185)
It's happening again. I'll be presenting 2025's data on Haloarchaeal methylation pattern, comparing outputs between Pacbio and ONT platforms at #ASMicrobe2026.
What do you think - microbial mechanism discovery or applied & environmental microbiology track?
🧫🦠
What do you think - microbial mechanism discovery or applied & environmental microbiology track?
🧫🦠
November 24, 2025 at 12:39 PM
It's happening again. I'll be presenting 2025's data on Haloarchaeal methylation pattern, comparing outputs between Pacbio and ONT platforms at #ASMicrobe2026.
What do you think - microbial mechanism discovery or applied & environmental microbiology track?
🧫🦠
What do you think - microbial mechanism discovery or applied & environmental microbiology track?
🧫🦠
Reposted by naturepoker
The Cost of Forgetting
by Chelsi — Vaccines have made a world that is safer and healthier. But, vaccines have made us comfortable enough to forget.
by Chelsi — Vaccines have made a world that is safer and healthier. But, vaccines have made us comfortable enough to forget.
The Cost of Forgetting
by Chelsi — Vaccines have made a world that is safer and healthier. But, vaccines have made us comfortable enough to forget.
smallthingsconsidered.blog
November 24, 2025 at 9:00 AM
The Cost of Forgetting
by Chelsi — Vaccines have made a world that is safer and healthier. But, vaccines have made us comfortable enough to forget.
by Chelsi — Vaccines have made a world that is safer and healthier. But, vaccines have made us comfortable enough to forget.
Reposted by naturepoker
New #ISEPpapers! Natural and artificial variations of the standard genetic code www.cell.com/current-biol... #Protists #TreeOfLife #Evolution #Microbes #Genetics
November 23, 2025 at 6:01 PM
New #ISEPpapers! Natural and artificial variations of the standard genetic code www.cell.com/current-biol... #Protists #TreeOfLife #Evolution #Microbes #Genetics
Oh this is fascinating. NA captive population of giraffes are extensively hybridized, and are not effective representatiom of the separate giraffe species in the wild.
Makes you wonder about current and future 'de-extinction' type experiments as well.
doi.org/10.1093/jher...
Makes you wonder about current and future 'de-extinction' type experiments as well.
doi.org/10.1093/jher...
🦒 Recent genomics research confirms four distinct giraffe species, revealing extensive hybridization in North American captive populations. To ensure effective conservation, authors recommend phasing out hybrids and creating new, genetically pure stocks through international collaboration.
November 23, 2025 at 6:30 PM
Oh this is fascinating. NA captive population of giraffes are extensively hybridized, and are not effective representatiom of the separate giraffe species in the wild.
Makes you wonder about current and future 'de-extinction' type experiments as well.
doi.org/10.1093/jher...
Makes you wonder about current and future 'de-extinction' type experiments as well.
doi.org/10.1093/jher...
Ok I'd actually love to hear people's take on this one. Vigorous skepticism about inferred trees (based on alignments) that eventually also require manual adjustment, and what that means for phylogeny is a curiously often encountered conversation for me these days.
🧬💻
🧬💻
I just keep reading this piece over and over again and...
arxiv.org/abs/1808.07717
arxiv.org/abs/1808.07717
Multiple Sequence Alignment is not a Solved Problem
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evide...
arxiv.org
November 23, 2025 at 6:17 PM
Ok I'd actually love to hear people's take on this one. Vigorous skepticism about inferred trees (based on alignments) that eventually also require manual adjustment, and what that means for phylogeny is a curiously often encountered conversation for me these days.
🧬💻
🧬💻
Reposted by naturepoker
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage
Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom
academic.oup.com
November 23, 2025 at 4:39 PM
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
This. Granted I might take deep, deep discount on more nvme drives.
November 23, 2025 at 5:56 PM
This. Granted I might take deep, deep discount on more nvme drives.
Hmm. I've been running an informal toy test comparing brute force alignment based #archaea gene annotation VS a 3rd party pipeline using structural predictions & search. Brute force method 'seems' to perform better in resolving function to hypothetical proteins. Not sure how this could be though🧬💻
November 23, 2025 at 2:41 PM
Hmm. I've been running an informal toy test comparing brute force alignment based #archaea gene annotation VS a 3rd party pipeline using structural predictions & search. Brute force method 'seems' to perform better in resolving function to hypothetical proteins. Not sure how this could be though🧬💻
Reposted by naturepoker
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
November 22, 2025 at 3:36 PM
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
Reposted by naturepoker
I’m glad to see they grew up to still have a happy and fulfilling life
November 23, 2025 at 1:00 PM
I’m glad to see they grew up to still have a happy and fulfilling life
This is a wonderful Sunday morning read. Also surprise Andrew Wyeth's passed away 2009 - it's practically yesterday.
A (Much) Closer Look at Christina’s World | Magazine | MoMA
www.moma.org/magazine/art...
A (Much) Closer Look at Christina’s World | Magazine | MoMA
www.moma.org/magazine/art...
A (Much) Closer Look at Christina’s World | Magazine | MoMA
See Andrew Wyeth’s most famous painting as never before: through the eyes of a conservation photographer.
www.moma.org
November 23, 2025 at 2:09 PM
This is a wonderful Sunday morning read. Also surprise Andrew Wyeth's passed away 2009 - it's practically yesterday.
A (Much) Closer Look at Christina’s World | Magazine | MoMA
www.moma.org/magazine/art...
A (Much) Closer Look at Christina’s World | Magazine | MoMA
www.moma.org/magazine/art...
This is an interesting one, though probably not unexpected. Now I'm having thoughts about annotation pipeline in my lab
🧫🦠 #archeasky
🧫🦠 #archeasky
An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 23, 2025 at 1:47 PM
This is an interesting one, though probably not unexpected. Now I'm having thoughts about annotation pipeline in my lab
🧫🦠 #archeasky
🧫🦠 #archeasky
Thinking about what to get after work this morning. Geez, anything not Dunkin donuts croissant might be out of my budget in the area of the city I'll be in. This sucks.
November 23, 2025 at 1:36 PM
Thinking about what to get after work this morning. Geez, anything not Dunkin donuts croissant might be out of my budget in the area of the city I'll be in. This sucks.
Great news. I've been using GlobDB for tracking distribution of a class of replicators across taxonomies. Highly, highly recommended for people looking for dereplicated dataset.
🧬💻
🧬💻
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:37 PM
Great news. I've been using GlobDB for tracking distribution of a class of replicators across taxonomies. Highly, highly recommended for people looking for dereplicated dataset.
🧬💻
🧬💻
On a different note, here's another street side used books stall pickup. $2 for the two books! Looking forward to going through them.
November 21, 2025 at 4:19 PM
On a different note, here's another street side used books stall pickup. $2 for the two books! Looking forward to going through them.
Reposted by naturepoker
Excited to share DupyliCate - our new tool for discovery and characterization of gene duplications:
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
DupyliCate - mining, classifying, and characterizing gene duplications
Paralogs, copies of a gene, form an important basis for novelty during evolution. Analysis of such gene duplications is important to understand the emergence of novel traits during evolution. DupyliCa...
doi.org
October 14, 2025 at 5:26 AM
Excited to share DupyliCate - our new tool for discovery and characterization of gene duplications:
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
"DupyliCate - mining, classifying, and characterizing gene duplications"
doi.org/10.1101/2025...
#Bioinformatics #Python #Genomics #Evolution
@puckerlab.bsky.social
No, research driven only by boredom and 'child like wonder' isn't a purer form of the craft. What spoiled nonsense is this? If you're bored of your life and looking for something to do that's fine. But don't define the whole darn field of independent/amateur research around your personality.
November 21, 2025 at 4:12 PM
No, research driven only by boredom and 'child like wonder' isn't a purer form of the craft. What spoiled nonsense is this? If you're bored of your life and looking for something to do that's fine. But don't define the whole darn field of independent/amateur research around your personality.
Hm I really need to start properly accounting for the times needed to download these massive databases now.
November 21, 2025 at 3:55 PM
Hm I really need to start properly accounting for the times needed to download these massive databases now.
Reposted by naturepoker
send this post to your friends who love cocks open.substack.com/pub/ryanmand...
potatoes have descended on new york city
peent
open.substack.com
November 21, 2025 at 12:02 PM